Eukaryotic retrotransposons are divided into two distinct classes of elements based on their structures: the long terminal repeat (LTR) retrotransposons and the LINE-like or non-LTR elements. See, Doolittle et al. (1989) Quart. Rev. Biol. 64:1–30; and Xiong and Eickbush (1990) EMBO J. 9:3353–3362. These element classes are related by the fact that each must undergo reverse transcription of an RNA intermediate to replicate, and each generally encodes its own reverse transcriptase. The LTR retrotransposons replicate by a mechanism resembling that of the retroviruses. See, Boeke and Sandmeyer (1991) Yeast transposable elements, in The Molecular and Cellular Biology of the Yeast Saccharomyces, ed. Broach, Jones, and Pringle, pp. 193–261 (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.). LTR retrotransposons typically use a specific tRNA to prime reverse transcription, and a linear cDNA is synthesized through a series of template transfers that require redundant LTR sequences at each end of the mRNA. This process occurs within a virus-like particle formed from proteins encoded by the retrotransposon mRNA. After reverse transcription, an integration complex is organized that directs the resulting cDNA to a new site in the genome of the host cell.
Phylogenetic analyses based on reverse transcriptase amino acid sequences have separated the LTR retrotransposons into two families: the Ty3/gypsy retrotransposons (Metaviridae), and the Ty1/copia elements (Pseudoviridae). See, Boeke et al. (1998) Metaviridae, in Virus Taxonomy: ICTV VIIth Report, ed. Murphy (Springer-Verlag, NY); and Boeke et al. (1998) Pseudoviridae, in Virus Taxonomy: ICTV VIIth Report, ed. Murphy (Springer Verlag, NY); Xiong and Eickbush supra. Although distinct, Ty3/gypsy elements are more closely related to retroviruses than to Ty1/copia elements. Ty3/gypsy elements share a similar genetic organization with the retroviruses, principally in the order of integrase and reverse transcriptase in their pol genes. Reverse transcriptase precedes integrase in the Ty3/gypsy elements, and this order is reversed for the Ty1/copia elements. In addition, some Ty3/gypsy elements have an extra open reading frame (ORF) encoding a polypeptide that is similar to retroviral envelope (env) proteins, which is required for viral infectivity. The Drosophila melanogaster gypsy retrotransposons encode an env-like ORF and can be transmitted between cells. See, Kim et al. (1994) Proc. Natl. Acad. Sci. USA 91:1285–1289; and Song et al. (1994) Genes Dev. 8:2046–2057. The retroviruses and the Ty3/gypsy retrotransposons that encode envelope-like proteins make up two distinct lineages of infectious LTR retroelements. The Ty3/gypsy elements have been further divided into two genera, the metaviruses and the errantiviruses, the latter including all elements with env-like genes. See, Boeke et al. Metaviridae (supra).
Retrotransposons have been extremely successful in plants. See, e.g., Bennetzen (1996) Trends Microbiol. 4:347–353; and Voytas (1996) Genetics 142:569–578. The enormous size of many plant genomes allows a great tolerance for repetitive DNA, a substantial proportion of which appears to be composed of retrotransposons. Because of their abundance, retrotransposons have undoubtedly influenced plant gene evolution. Retrotransposons can cause mutations in coding sequences (Grandbastien et al. (1989) Nature 337:376–380; Hirochika et al. (1996) Proc. Natl. Acad. Sci. USA 93:7783–7788; and Purugganan and Wessler (1994) Proc. Natl. Acad. Sci. USA 91:11674–11678), and the promoter regions of some plant genes contain relics of retrotransposon insertions that contribute transcriptional regulatory sequences. See, White et al. (1994) Proc. Natl. Acad. Sci. USA 91:11792–11796. Retrotransposons also can generate gene duplications, as repetitive retrotransposon sequences provide substrates for unequal crossing over. Such an event is thought to have caused a zein gene duplication in maize (White et al., supra). Cellular mRNAs occasionally are reverse transcribed, and the resultant cDNA recombines into the genome to give rise to new genes or, more frequently, cDNA pseudogenes. See, Maestre et al. (1995) EMBO J. 14:6333–6338. The transduction of gene sequences during reverse transcription, which produced the oncogenic retroviruses, also has been documented for a plant retrotransposon (Bureau et al. (1994) Cell 77:479–480; and Jin and Bennetzen (1994) Plant Cell 6:1177 1186). A maize Bs1 insertion in Adh1 carries part of an ATPase gene and is the only known example of a retrotransposon-mediated gene transduction event.
Plant genomes can encode representatives of the two major lineages of LTR retrotransposons that have been identified in other eukaryotes. Among these are numerous examples of Ty1/copia elements (see, e.g., Konieczny et al. (1991) Genetics 127:801–809; Voytas and Ausubel (1988) Nature 336:242–244; and Voytas et al. (1990) Genetics 126:713–721). Also prevalent are Ty3/gypsy elements that are member of the genus Metaviridae (Smyth et al. 1989 Proc. Natl. Acad. Sci. USA 86:5015–5019; Purugganan and Wessler (1994) Proc. Natl. Acad. Sci. USA 91:11674–11678; and Su and Brown (1997) Plasmid 38:148–157). As stated above, some metaviruses, including plant metaviruses, contain an envelope gene characteristic of the retroviruses. It has been suggested that the envelope gene may be required for cell-to-cell transmission of plant metaviruses (Bennetzen, supra). The uncertainty, however, has been described with respect to Cyclops, a retroelement identified from pea: “Since genes encoding ENV functions are very heterogeneous at the sequence level and difficult to identify by homology even between retroviruses, the possibility cannot be completely excluded at the present time that the 3′ ORF of Cyclops is, in fact, an env gene and, hence, Cyclops is a retrovirus or a descendant of one.” Chavanne et al. (1998) Plant Mol. Biol. 37:363–375.
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